From 40f4af189a651790f9e6d7057e8dcce942bee266 Mon Sep 17 00:00:00 2001
From: Kim Rutherford <kmr@aska.gen.nz>
Date: Tue, 11 Jun 2024 11:29:13 +1200
Subject: [PATCH] Remove unused organisms after updating

After updating genes using the latest species_strain_map, clean up
unused organisms.

Refs pombase/canto#2831
---
 etc/reapply_species_strain_map.pl | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/etc/reapply_species_strain_map.pl b/etc/reapply_species_strain_map.pl
index 2e47d5c19..2ece7e3a2 100755
--- a/etc/reapply_species_strain_map.pl
+++ b/etc/reapply_species_strain_map.pl
@@ -102,8 +102,29 @@ BEGIN
       $gene->update();
     }
   }
+
+  # Remove unused organisms
+  $organism_rs = $curs_schema->resultset('Organism');
+
+  while (defined (my $organism = $organism_rs->next())) {
+    if ($organism->genes()->count() == 0 &&
+        $organism->genotypes()->count() == 0) {
+      my $strain_rs = $organism->strains();
+
+      while (defined (my $strain = $strain_rs->next())) {
+        if ($strain->genotypes()->count() == 0) {
+          $strain->delete();
+        }
+      }
+
+      if ($strain_rs->count() == 0) {
+        $organism->delete();
+      }
+    }
+  }
 };
 
+
 my $load_util = Canto::Track::LoadUtil->new(schema => $schema);